What does it mean to be correlated? Bob made some sugestions for the caculation of phenotype and the slope of the interaction. prob_of_survive = 1.0/(1+exp(-((compair_pheno-c)/w))) In this equation c=0 and w=10. W may be too high, which could limit interaction/coevolution outcomes. The way phenotypes are defined might be creating a multiplicative effect: exp(ind.sumOfMutationsOfType(m2)/10))
I created a simulation study to observe the co-evolutionary outcome of the newt-snake interaction with different genetic architectures (GAs) in a spatial setting. I hypothesized that we would see an interaction (co-evolutionary arms race) between newt and snake phenotype under some GA combinations when newts and snakes were evolving over geographical space. Each GA is paired with another GA creating 16 combinations.
GA1 experiment values:
Each GA combination and trial has its own msprime simulation. I ran 3 experiments a) no exp in the phenotype, b) lower w and, c) both no exp and a lower w
many of the experiments did not run to completion (i will run this part 3 times)
## All cor, lit, and grid files exist!
## This program will now end!
## All cor, lit, and grid files exist!
## This program will now end!
## All cor, lit, and grid files exist!
## This program will now end!
## Group.1 x
## 1 1e-08_0.005_1e-08_0.005 -1.51426587
## 2 1e-08_0.005_1e-09_0.05 -2.46502318
## 3 1e-08_0.005_1e-10_0.5 -2.95261240
## 4 1e-08_0.005_1e-11_5 -1.20777647
## 5 1e-09_0.05_1e-08_0.005 -0.21336817
## 6 1e-09_0.05_1e-09_0.05 -1.19346049
## 7 1e-09_0.05_1e-10_0.5 -1.35969385
## 8 1e-09_0.05_1e-11_5 -1.06953203
## 9 1e-10_0.5_1e-08_0.005 -0.16383653
## 10 1e-10_0.5_1e-09_0.05 -0.27008539
## 11 1e-10_0.5_1e-10_0.5 -0.03165683
## 12 1e-10_0.5_1e-11_5 0.40039860
## 13 1e-11_5_1e-08_0.005 -0.46647760
## 14 1e-11_5_1e-09_0.05 -0.31799699
## 15 1e-11_5_1e-10_0.5 0.55002347
## 16 1e-11_5_1e-11_5 1.69392449
## Group.1 x
## 1 1e-08_0.005_1e-08_0.005 -0.07560489
## 2 1e-08_0.005_1e-09_0.05 -0.45206573
## 3 1e-08_0.005_1e-10_0.5 -0.93236044
## 4 1e-08_0.005_1e-11_5 -1.34750726
## 5 1e-09_0.05_1e-08_0.005 0.29741783
## 6 1e-09_0.05_1e-09_0.05 -0.41278289
## 7 1e-09_0.05_1e-10_0.5 -0.27036120
## 8 1e-09_0.05_1e-11_5 0.70687010
## 9 1e-10_0.5_1e-08_0.005 1.57745179
## 10 1e-10_0.5_1e-09_0.05 -0.94392931
## 11 1e-10_0.5_1e-10_0.5 -0.50809115
## 12 1e-10_0.5_1e-11_5 -0.63724476
## 13 1e-11_5_1e-08_0.005 1.17201401
## 14 1e-11_5_1e-09_0.05 -1.26567646
## 15 1e-11_5_1e-10_0.5 -0.42440551
## 16 1e-11_5_1e-11_5 -0.65839029
## Group.1 x
## 1 1e-08_0.005_1e-08_0.005 -4.1473108
## 2 1e-08_0.005_1e-09_0.05 -4.4691855
## 3 1e-08_0.005_1e-10_0.5 -4.7064956
## 4 1e-08_0.005_1e-11_5 -4.8079958
## 5 1e-09_0.05_1e-08_0.005 -3.0306376
## 6 1e-09_0.05_1e-09_0.05 -3.8945754
## 7 1e-09_0.05_1e-10_0.5 -4.2043963
## 8 1e-09_0.05_1e-11_5 -4.3995742
## 9 1e-10_0.5_1e-08_0.005 -0.2254921
## 10 1e-10_0.5_1e-09_0.05 -1.3878429
## 11 1e-10_0.5_1e-10_0.5 -2.0643520
## 12 1e-10_0.5_1e-11_5 -2.0162477
## 13 1e-11_5_1e-08_0.005 0.7723211
## 14 1e-11_5_1e-09_0.05 -0.5933950
## 15 1e-11_5_1e-10_0.5 -1.0389160
## 16 1e-11_5_1e-11_5 -2.0689460
HEREREERERERER
## [1] "pattern 1e-10_0.5_1e-10_0.5_3"
## [1] "Cor between average snake pheno and local cor -0.0509598684052669"
## [1] "Cor between average newt pheno and local cor -0.0616088122733205"
## [1] "Cor between average dif pheno and local cor 0.024753510228788"
## [1] "Cor between newt pheno and snake 0.452967125117761"
## [1] "pattern 1e-09_0.05_1e-08_0.005_0"
## [1] "Cor between average snake pheno and local cor NA"
## [1] "Cor between average newt pheno and local cor NA"
## [1] "Cor between average dif pheno and local cor NA"
## [1] "Cor between newt pheno and snake 0.857207147586658"
## [1] "pattern 1e-09_0.05_1e-10_0.5_2"
## [1] "Cor between average snake pheno and local cor NA"
## [1] "Cor between average newt pheno and local cor NA"
## [1] "Cor between average dif pheno and local cor NA"
## [1] "Cor between newt pheno and snake 0.845226168052167"
## [1] "pattern 1e-08_0.005_1e-08_0.005_3"
## [1] "Cor between average snake pheno and local cor -0.239884385890239"
## [1] "Cor between average newt pheno and local cor -0.224294577594795"
## [1] "Cor between average dif pheno and local cor -0.380489332922223"
## [1] "Cor between newt pheno and snake 0.998670614771072"
## [1] "pattern 1e-10_0.5_1e-08_0.005_1"
## [1] "Cor between average snake pheno and local cor NA"
## [1] "Cor between average newt pheno and local cor NA"
## [1] "Cor between average dif pheno and local cor NA"
## [1] "Cor between newt pheno and snake 0.340665480109894"
## [1] "pattern 1e-11_5_1e-09_0.05_2"
## [1] "Cor between average snake pheno and local cor -0.170477954353067"
## [1] "Cor between average newt pheno and local cor -0.258054361352234"
## [1] "Cor between average dif pheno and local cor 0.292227184956155"
## [1] "Cor between newt pheno and snake 0.90110923231345"
## [1] "pattern 1e-10_0.5_1e-11_5_2"
## [1] "Cor between average snake pheno and local cor -0.00510092147501471"
## [1] "Cor between average newt pheno and local cor 0.0845087520427481"
## [1] "Cor between average dif pheno and local cor -0.0741149559013315"
## [1] "Cor between newt pheno and snake 0.850957045510594"
## [1] "pattern 1e-10_0.5_1e-11_5_3"
## [1] "Cor between average snake pheno and local cor -0.00639271957395647"
## [1] "Cor between average newt pheno and local cor -0.100219392868776"
## [1] "Cor between average dif pheno and local cor 0.066755299995335"
## [1] "Cor between newt pheno and snake 0.691152279038801"
## [1] "pattern 1e-10_0.5_1e-10_0.5_2"
## [1] "Cor between average snake pheno and local cor -0.119820551416607"
## [1] "Cor between average newt pheno and local cor -0.112544845130158"
## [1] "Cor between average dif pheno and local cor -0.103077399834705"
## [1] "Cor between newt pheno and snake 0.891358848348999"